Currently, laser-scanning, photomultiplier tube (PMT) based imagers are most commonly used for quantification of genome and proteome data from gene and protein micro arrays. Currently, the user of one of these scanners must set the gain of the detector differently for each slide, in order to optimally scan the slide. This is especially the case if the slide preparation is different for each slide, or if the gene profile on the microarray slide is very different from one experiment to the next. The variance in gain setting prevents users from auto-loading multiple slides, and automatically scanning and analyzing multiple slides at once.
U.S. patent application Ser. No. 09/596,391, entitled “An Automated, CCD-Based Microarray Imaging System”, assigned to Genomic Solutions Inc, hereby incorporated by reference, describes an auto-exposure method for auto loading multiple slides. Here, a linear detector such as a CCD camera and a stage automatically introduces multiple samples. Sample introduction, calculation of exposure times through an autoexpose technique, collection, and storage of the data are all accomplished under computer control. A user can load the instrument up with multiple samples, pick an appropriate protocol, and walk away from the instrument as it processes many samples.
U.S. patent application Ser. No. 09/566,048 (PCT/US00/12220) entitled “Laser Based Optical Scanning System” and U.S. Provisional App. No. 60/258,440 “Dark-Field Laser Scanner”, hereby incorporated by reference, describes laser scanning instrumentation specifically designed for automated sample introduction. Here, the laser illuminates one point on the sample at a time, and one or more photomultiplier tubes (PMT) measure the fluorescence at that point. An image arises when the point is scanned in a raster pattern over the sample and the measurements are arranged in a two-dimensional array. A quantifiable image requires that the gain of the PMT be constant over the course of the scan. To vary the overall brightness of the image, the PMT gain can be adjusted between scans. With the scanner and PMT gain under computer control, automatic optimization of image brightness is possible.
Because micro-array and other samples can vary greatly in their emitted signal brightness, depending on how they are prepared, the detector gain setting often must be set differently, even for similar samples. Setting of this gain often requires user intervention for each sample. Ideally, the instrument would be able to automatically determine the correct gain setting. However, this is a complex task when the detector output is not linearly related to the gain setting. In a PMT for instance, the response to light is linearly related to the number of photons impinging on the tube, at a specified gain setting. However, the relationship between the gain setting and the output of the PMT is very non-linear.